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Hi,
oXygen allows you to store the options at project level (see the Project Options option on most preferences pages). You can define your formatting options and then store them at project level. If all your team members use the same project to edit the files then they will all get the same formatting options and you will be able to work with concurrent versioning systems without having the issues you described. This is what we use for the oXygen user manual and for the oXygen website (that is authored as an XML document) and it works pretty well.
Hope that helps,
George
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